I go on Github, and the files aren't there. Other files were committed and show up, but two folders do not have matching content. The files exist in other but not in master. To clarify, the files were not new. But I thought that merging would at least copy files to master if they dont exist!

Hi, are you sure your files have been commited? There's no reason Git would hide them away during the merge. Can you post all the commands you've made? (This will help find out the problem)
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Simon BoudriasNov 29 '12 at 3:29

git add ., git commit -m 'something', git push, git checkout, git merge. Probably in every order by now and many times
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AJcodezNov 29 '12 at 3:38

And what happen if you do git status in other branch ?
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Simon BoudriasNov 29 '12 at 3:53

In branch master, execute git branch --merged, if it's not listing the other branch, then the other branch is not merged with master.
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Karthik BoseNov 29 '12 at 4:09

If you're getting different results, you're either missing a step, putting an extra step somewhere, or you're getting some sort of error you're not telling us about, like a merge conflict. We have no way of knowing why something so basic isn't working for you unless you post the exact commands and output you're getting, like I did above.